An optimized GATK4 pipeline for Plasmodium falciparum whole genome sequencing variant calling and analysis

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BACKGROUND: Accurate variant calls from whole genome sequencing (WGS) of Plasmodium falciparum infections are crucial in malaria population genomics. Here a falciparum variant calling pipeline based on GATK version 4 (GATK4) was optimized and applied to 6626 public Illumina WGS samples. METHODS: Con...

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Detalles Bibliográficos
Autores principales: Niaré, Karamoko, Greenhouse, Bryan, Bailey, Jeffrey A.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2023
Materias:
Methodology
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10327343/
https://www.ncbi.nlm.nih.gov/pubmed/37420214
http://dx.doi.org/10.1186/s12936-023-04632-0

Internet

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10327343/
https://www.ncbi.nlm.nih.gov/pubmed/37420214
http://dx.doi.org/10.1186/s12936-023-04632-0

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